Dear R-devel,
We are planning a package that provides R interface to cuBLAS (CUDA accelerated
BLAS). Due to CUDA's requirement, we are wondering if anyone can provide some
guidance and suggestions on best way forward.
CUDA lists Visual Studio as a requirement on Windows, and it looks like no o
Never mind. Found the problem: The package has been missing a subset method
for the "lp" class since [...]. Adding "[.lp" solved the problem.
Cheers,
Andy
-Original Message-
From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On
Behal
Dear R-devel,
I recent got a bug report from a locfit user about the use of the subset
argument when calling locfit(). Basically the symptom is that the following
two calls should produce the same result, but they don't:
locfit(y ~ lp(x, h=1), data=subset(dat, x > 1))
locfit(y ~ lp(x, h=1), da
From: Max Kuhn
>
> Working on the caret package has exposed me to the wide variety of
> approaches that different authors have taken to creating predictive
> modeling functions (aka machine learning)(aka pattern recognition).
>
> I suspect that many package authors are neophyte R users and are
>
> From: Simon Urbanek
>
> On Sep 17, 2010, at 1:22 PM, Liaw, Andy wrote:
>
> > From: Liaw, Andy
> >>
> >> From: Prof Brian Ripley
> >>>
> >>> On Fri, 27 Aug 2010, peter dalgaard wrote:
> >>>
> >>>&g
From: Liaw, Andy
>
> From: Prof Brian Ripley
> >
> > On Fri, 27 Aug 2010, peter dalgaard wrote:
> >
> > >
> > > On Aug 27, 2010, at 2:44 PM, Liaw, Andy wrote:
> > >
> > >> I'd very much appreciate guidance on this. A user
From: Uwe Ligges
>
>
> On 29.08.2010 22:34, Kyle Matoba wrote:
> > All,
> >
> > I just finished the process of build a package for the
> first time and found
> > it characteristically (for R) very straightforward and well
> documented.
> >
> > Whenever I deal with open source software I always
From: Prof Brian Ripley
>
> On Fri, 27 Aug 2010, peter dalgaard wrote:
>
> >
> > On Aug 27, 2010, at 2:44 PM, Liaw, Andy wrote:
> >
> >> I'd very much appreciate guidance on this. A user
> reported that the
> >> as.double() coercion used i
I'd very much appreciate guidance on this. A user reported that the
as.double() coercion used inside the .C() call for a function in my
package (specifically, randomForest:::predict.randomForest()) is
taking up significant amount of time when called repeatedly, and
Removing some of these reduce
From: spencerg
>
> Thank you all for your suggestions. My goal with this
> is to make
> it as easy as possible for R users to find what they want in
> contributed
> packages. A referee for our "R Journal" manuscript complained that
> "RSiteSearch.function" was too much to type, sugges
I don't know if this applies to Seija's case, but one instance that I've ran
into when problem arose only with -O3 is uninitialized variables/arrays.
Adding the initialization fixed the problem. Just one thing to check, I guess.
Best,
Andy
From: Prof Brian Ripley
>
> It is likely that this i
p = gsub( rx, "\\2", txt ),
> > description = gsub( rx, "\\3", txt ),
> > stringsAsFactors = FALSE
> > )
> > out$group <- sub( "...", ".*", out$group, fixed = TRUE )
> > out
> > }
> >
> > I&#
From: Jonathan Baron
>
> On 05/07/09 13:48, Liaw, Andy wrote:
> > From: Duncan Murdoch
> > > I'll incorporate the changes if you like.
>
> Yes. Please do. I understand that it won't take effect for a while.
> When it does, I'll change my site
From: Duncan Murdoch
>
> On 5/7/2009 10:18 AM, Jonathan Baron wrote:
> > On 05/07/09 10:05, Liaw, Andy wrote:
> >> Can someone in R Core please take a look at the attached patches to
> >> RSiteSearch() and its help page? I guess Jon is planning
> some changes
&
From: Liaw, Andy
>
> From: Liaw, Andy
> >
> > Can someone in R Core please take a look at the attached patches to
> > RSiteSearch() and its help page? I guess Jon is planning
> some changes
> > on his site.
>
> Apparently the attachments were stripped
From: Liaw, Andy
>
> Can someone in R Core please take a look at the attached patches to
> RSiteSearch() and its help page? I guess Jon is planning some changes
> on his site.
Apparently the attachments were stripped off the first time. Here's a
second try.
I've a
Can someone in R Core please take a look at the attached patches to
RSiteSearch() and its help page? I guess Jon is planning some changes
on his site. Jon: could you elaborate on what the patch does?
Best,
Andy
Notice: This e-mail message, together with any attachments, contains
information
Just expressing MHO: The algorithm cannot give predictions in classes
that never appear in the training data, so any entries in the loss
matrix related to such classes are irrelevant w.r.t. the training data.
They should be removed before feeding to rpart (or any other algorithm
that can make use
[I believe few users manipulate formulae and model frames like this, so
I'm posting here instead of R-help.]
I just found out that model.frame() includes all terms, including those
preceded by "-" in the formula, in its output (as mentioned on its help
page). Is there a recommended way of excludi
Hello everyone,
I'm trying to update the locfit package so that it passes package check
in R 2.6.0. However, the check seems to think some of the functions
with dot in the names are S3 methods (thus warns about the format of the
\usage{} part) when they are not. Can anyone recommend a workaround
(I see this in both R-patched r43124 and R-devel r43233.)
In the Argument section of ?mean:
trim the fraction (0 to 0.5) of observations to be trimmed from each
end of x before the mean is computed. Values outside that range are
taken as the nearest endpoint.
Then in the Value section:
If
In the "Value" section of ?aperm, I see:
`... In each case other attributes are copied from a.'
However:
R> f <- factor(sample(letters[1:2], 10, replace=TRUE))
R> dim(f) <- c(5, 2)
R> t(f)
[,1] [,2] [,3] [,4] [,5]
[1,] aabbb
[2,] aabaa
Levels: a b
R> ap
It's the quoting character(s). This following seems to read the file in
correctly:
R> DF <- read.table("http://llmpp.nih.gov/DLBCL/NEJM_Web_Fig1data";,
+ header = TRUE, sep = "\t", quote="")
R> str(DF)
'data.frame': 7399 obs. of 295 variables:
[...]
If I have to guess, it's
Given that the behavior is exactly as I expected it be, I would call
that "feature" (and IMHO not a very special one). The two data frames
are just different (try str() on them: A in dd is factor, while A in
dd2 is character), so I don't know why you'd expect unlist() on them to
give you the same
I think many would object to automatic check at every start-up. For the
issue at hand, perhaps a check inside bug.report() would go a long way?
Just an idea...
Andy
From: Barry Rowlingson
>
> Since many posts to R-devel/help invoke this response:
>
> Prof Brian Ripley wrote:
> > Please, use t
Dear R-devel,
Kurt had alerted me to the problem that the randomForest package that I
maintain has been failing checks in R-devel. However, I just can't see
why or where it's failing. I'd very much appreciate any pointer.
The failure occur when running the example code in varImpPlot.Rd:
> varI
From: Evan Cooch
>
> Greetings -
>
> A quick perusal of some of the posts to this maillist suggest
> the level of the questions is probably beyond someone working
> at my level, but at the risk of looking foolish publicly
> (something I find I get increasingly comfortable with as I
> get olde
If I'm not mistaken, this works as documented. As an example (typed
directly into the Rgui console on WinXP):
R> f <- function() {
+ browser()
+ cat("I'm here!\n")
+ cat("I'm still here!\n")
+ }
R> f()
Called from: f()
Browse[1]> ## where to?
I'm here!
I'm still here!
which I think i
Dear DevelopeRs,
I'd like to ask those who develop R packages with compiled code to please
try avoiding dependency on GCC (gcc/g77/gfortran/g++) specific features in
the code, for the simple reason that there are non-GCC compilers out there
that might choke on such features.
I found this out back
From: Uwe Ligges
>
> Pfaff, Bernhard Dr. wrote:
>
> > Pfaff, Bernhard Dr. wrote:
> >
> >
> >>Pfaff, Bernhard Dr. wrote:
> >>
> >>
> >>
> >>>Dear R-Devel subscriber,
> >>>
> >>>first, let me express my thank to the R-Core team for the new
> >>>release!
> >>
> >>I
> >>
> >>
> >>>appreciate their
I was under the impression that PP communicates with R via SOAP, but
what do I know...
If I didn't read your description wrong, the "R Collection" contains
PP code (PilotScript?) for generating R code to be run by R, but does
not include R itself. If that's the case, I don't think it has any
lic
From: Bill Dunlap
>
> On Thu, 13 Apr 2006, Prof Brian Ripley wrote:
>
> > On Thu, 13 Apr 2006, Peter Ruckdeschel wrote:
> >
> > > Hi R-devels,
> > >
> > > in "Writing R extensions" as well as in the help
> > > to .onAttach(), you mention that one could
> > > use this function to issue a start-up
From: Prof Brian Ripley
>
> On Thu, 13 Apr 2006, Peter Ruckdeschel wrote:
>
> > Hi R-devels,
> >
> > in "Writing R extensions" as well as in the help
> > to .onAttach(), you mention that one could
> > use this function to issue a start-up message/banner
> > for the package.
> >
> > My little wish
From: Romain Francois
>
> Hi,
>
> I have a couple of questions:
> * would it be possible to add more information on the history, for
> example the number of the command and a timestamp. With the number of
> command, one could do some stuff like in a terminal to recall
> a specific
> command :
Ditto for me, with the following exceptions:
- I always use save(..., compress=TRUE), without exception.
- The only time I'd use save.image() is when I need to break a remote
connection on short notice.
- I have not used options() to set the default simply because I have not
figured out how exactl
That looks like the symptom of not following the documentation when trying
to build packages on Windows. (You have not stated the platform.) In that
case please check and see if you have the tools in Rtools.zip installed and
on the PATH.
Andy
From: Steve Su
>
> Dear All,
>
>
>
> I was tryi
Thanks to Brian, I can now get PGI 6.1 to build R-devel
(2006-03-13 r37533) and pass make check-all, using the
config flags I showed in my original post. I will try
to re-build with optimizing flags, and report back if I
run into problems there.
Best,
Andy
From: Jennifer Lai
>
> Jennifer La
Dear R-devel,
[I'm not sure if this is appropriate for R-devel. If not, I'm more than
happy to move it to R-help.]
As those of you who saw my post on R-help know, I've been trying to build
R-patched on a dual Opteron box running Scyld Beowulf, using the PGI 6.1
compilers. The build went fine, b
From: Dirk Eddelbuettel
>
> On 7 March 2006 at 10:55, Hin-Tak Leung wrote:
> | I have given up on "R" with any topic on Google quite some time ago
> | (because bits from fragmented postscript/pdf files show up, for
> | example) - but using "r-devel" with topic normally gives me enough.
> | YMMV
Paul,
I think what you're seeing is the performance gap between 64-bit binary and
32-bit binary on x86_64. I believe Prof. Ripley had mentioned this several
times in the past.
I do remember back when I was playing with optimized BLAS with R on 32-bit
Linux that I've seen something similar to wha
The last time I tried I didn't have much luck. The gprof manual I could
find seems to indicate that it can not profile code that are dynamically
loaded. (I was trying on Linux.) The R source seems to hint otherwise.
I'd very much appreciate pointers as well.
Andy
From: Ross Boylan
>
> Does an
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Duncan Murdoch
> Sent: Saturday, February 04, 2006 1:23 PM
> To: Andrew Finley
> Cc: r-devel@r-project.org
> Subject: Re: [Rd] Rprintf loop status does not print under windows
>
>
> On 2/4/2006 1:14
1. This is _not_ a bug in R itself. Please don't use R's bug reporting
system for contributed packages.
2. This is _not_ a bug in svm() in `e1071'. I believe you forgot to take
sqrt.
3. You really should use the `tot.MSE' component rather than the mean of
the `MSE' component, but this is only
Why isn't substitute(x, parent.frame()) enough? parse(deparse()) seems
redundant...
Andy
From: hadley wickham
>
> I'm trying to retrieve an unevalated argument (a list in particular).
> I can do this easily when I call the function directly:
>
> a1 <- function(x) match.call()$x
>
> > a1(list
From: [EMAIL PROTECTED]
>
> On 30-Jan-06 Roger D. Peng wrote:
> > Well shared! :) Maybe better yet,
> >
> > "Before I begin this talk, I'd like to 'attach("nano")'".
> >
> > -roger
>
> And, at the end of the talk:
>
>"Save workspace image? [y/n/c]: "
Nah! Always use q("no") or start R w
From: Greg Kochanski
>
> Achim Zeileis wrote:
> > On Mon, 30 Jan 2006, Greg Kochanski wrote:
> >
> >
> >>The bug is that the software produces results that could
> >>lead to the wrong conclusion in a research paper,
> >>or could lead the readers of the research paper to
> >>an erroneous belief.
From: Kasper Daniel Hansen
>
> First: this is not a bug, more a feature request.
>
> Secondly, even if it was a bug, it is _not_ a bug in R, please read
> the posting rules for bugs. Now a member of R-core has to use
> valuable time to clean up after your bug report.
>
> Correspondence such
From: Kjetil Brinchmann Halvorsen
>
> Prof Brian Ripley wrote:
> > Quite a while back we set the goal of running R in 16Mb
> RAM, as people (I
> > think Kjetil) had teaching labs that small.
>
> It's a while since I actually har R used on such small
> machines, I think
> 64 MB is quite accepta
See the `Value' section of ?.C. Also, it's better to use the i/o provided
by the R API; i.e., something like:
#include "R.h"
void helloworld() {
Rprintf("Hello world!\n");
}
Andy
From: Romain Francois
>
> Hi,
>
> I'm trying to build a simple R package 'helloWorld' with just one
> funct
If you haven't seen this in your math courses, perhaps this would help:
http://en.wikipedia.org/wiki/Empty_set
which says, in part:
Operations on the empty set
Operations performed on the empty set (as a set of things to be operated
upon) can also be confusing. (Such operations are nullary oper
Just one call to each that enclose the RNG calls will do, I believe.
Andy
From: Tib
>
> Greetings,
>
> I am trying to write a C++ subroutine of my random number
> generator. Based
> on tutorial in Writing R Extensions, one should call
> GetRNGstate() before
> and PutRNGstate() after calling
I believe Gabor was referring to this:
http://tolstoy.newcastle.edu.au/R/devel/05/05/0837.html
Andy
From: Hin-Tak Leung
>
> Gabor Grothendieck wrote:
> > There was nothing attached in the copy that came through
> > to me.
>
> I like to see that patch also.
>
> > By the way, there was some dis
I suppose one can make use of slice.index():
> array(x[slice.index(x, 1) == 1], dim(x)[-1])
[,1] [,2]
[1,]1 13
[2,]5 17
[3,]9 21
Andy
> From: Henrik Bengtsson
>
> Hi,
>
> is there a function in R already doing what I try to do below:
>
> # Let 'x' be an array with *any
From: [EMAIL PROTECTED]
>
> On Tuesday 22 November 2005 12:55, [EMAIL PROTECTED] wrote:
[snip]
> > Since it is unstable and=20
> > unreleased, such things are by definition not bugs in R.
>
> Sorry, I did not know this. I thought that my report could help you.
> The next time when I will find a
> From: Hin-Tak Leung
>
> Izmirlian, Grant (NIH/NCI) wrote:
>
> > The only interesting feature is that the tree structure has been
> > implemented in C. Its a neater way to carry stuff around and I am
> > guessing would make future implementation easier.
> >
> > Because of its inherent redundan
Fritz gave a talk on S4 using pixmap as example at useR! 2004. You might
want to start with that. The slides should be on the useR! 2004 web site.
Andy
> From: Jeff Enos
>
> Thanks to Dirk Eddelbuettel, Matthias Kohl, Professor Ripley, and
> Bernhard Pfaff for their helpful reponses.
>
> Here
> From: Thomas Lumley
>
> On Sun, 30 Oct 2005, Jonathan Rougier wrote:
>
> > I'm not sure about this. Perhaps I am a dinosaur, but my feeling is
> > that if people are writing functions in R that might be subject to
> > simple operations like outer products, then they ought to be writing
> > vec
> From: Hin-Tak Leung
>
> Gabor Grothendieck wrote:
> > I wonder if the software here:
> >
> > http://morte.jedrea.com/~jedwin/projects/chmlib/
> >
> > or at any of the links on that page might allow elimination of the
> > need for separately downloading the Microsoft Help compiler --
> > which
This is in R-exts. If the Fortran subroutine is called `dqrfit', you would
use something like:
F77_CALL(dqrfit)(...);
All arguments need to be pointers, as Fortran passes by reference.
Andy
> From: James Bullard
>
> Hello, I had a question about calling some of R's fortran
> routines from C.
> From: Philippe Grosjean
>
> Duncan,
>
> I agree totally with you on all points, now that we clarified our
> respective ideas. I am afraid I probably agree also with your last
> point, from a theoretical point-of-view ("I still think we need more
> glue and am working on that while we continu
Where in ?cor do you see the na.rm argument? Mine says:
cor(x, y = NULL, use = "all.obs",
method = c("pearson", "kendall", "spearman"))
There's na.rm on that page, but that's for var(). Please read the R FAQ
more carefully about reporting bugs.
Andy
> From: [EMAIL PROTECTED]
>
> Full_Na
Apologies for the coming to this late...
1. By now I hope Somkiat has realized that R-bugs is not the place to
report problems in contributed packages. Please direct such reports to
the package maintainer.
2. This is really user error. predict() expect the newdata to be a data
frame containing
Dear R-devel,
I'm working on Prof. Loader's new version of locfit to try to get it
pass R CMD check. I'm almost there, but I have a problem with some Rd
files that I hope some one can help me resolve. Here's an example:
In the package there's a function called locfit.censor(). This function
ca
> From: Peter Dalgaard
>
> [EMAIL PROTECTED] writes:
>
> > Dette er en melding med flere deler i MIME-format.
> > --=_alternative 004613C000257091_=
> > Content-Type: text/plain; charset="US-ASCII"
> >
> > And some more informastion I forgot.
> > R does not crash if I write out the formula:
> >
The `problem' is that sort() does not doing anything special when given
a matrix: it only treat it as a vector. After sorting, it copies
attributes of the original input to the output. Since dimnames are
attributes, they get copied as is.
Try:
> y <- matrix(8:1, 4, 2, dimnames=list(LETTERS[1:4]
Dear R-devel,
I recall that there used to be a mechanism to get around the requirement
that all objects in a package have associated documentation; i.e., a way to
specify a list of objects (mostly functions) that are not considered as part
of the package API. Is this still available? I cannot fi
> From: r-devel
>
> Full_Name: Frank Wagner
> Version: R 2.1.1
> OS: Windows
> Submission from: (NULL) (193.174.73.34)
>
>
> Hi,
> The pdf file R-intro descripe on page 27 that lists can be
> extended by adding
> numbers.
> Unfortunately, it's not working
> ## example :
>
> # if i did not dec
I can only say that the last time I tried linking ACML to R, it did quite a
bit worse than Goto's BLAS.
Andy
> From: Jennifer Lai
>
> Hi,
> Has anyone had any luck in using portland group compiler
> to build
> R(-devel) with AMD's pgi compiled ACML library? I've downloaded the
> packag
Do you mean something like:
http://cran.r-project.org/src/contrib/Descriptions/RColorBrewer.html
?
Andy
> From: Peter Kleiweg
>
>
> Anyone who is interested in using optimal colour palettes should
> look at the work of Cindy Brewer: www.colorbrewer.org
>
> I have written code to use her colour
The issue is not with boxplot, but with split. boxplot.formula()
calls boxplot(split(split(mf[[response]], mf[-response]), ...),
but look at what split() returns when there are empty levels in
the factor:
> f <- factor(gl(3, 6), levels=1:5)
> y <- rnorm(f)
> split(y, f)
$"1"
[1] 0.4832124 1.192
I don't get the point. ?by says:
FUN a function to be applied to data frame subsets of data.
It doesn't say FUN can be a character, and by(iris, iris$Species, summary)
works as expected.
Andy
> From: Gabor Grothendieck
>
> I noticed that, unlike similar functions, 'by' does not use
> match.
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